Atomistry » Rhodium » PDB 165d-6wrm » 2zur
Atomistry »
  Rhodium »
    PDB 165d-6wrm »
      2zur »

Rhodium in PDB 2zur: Crystal Structure of Rh(Nbd)/Apo-Fr

Protein crystallography data

The structure of Crystal Structure of Rh(Nbd)/Apo-Fr, PDB code: 2zur was solved by S.Abe, K.Hirata, T.Ueno, N.Shimizu, M.Yamamoto, M.Takata, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.01 / 1.80
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.276, 181.276, 181.276, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.6

Other elements in 2zur:

The structure of Crystal Structure of Rh(Nbd)/Apo-Fr also contains other interesting chemical elements:

Cadmium (Cd) 5 atoms

Rhodium Binding Sites:

The binding sites of Rhodium atom in the Crystal Structure of Rh(Nbd)/Apo-Fr (pdb code 2zur). This binding sites where shown within 5.0 Angstroms radius around Rhodium atom.
In total 3 binding sites of Rhodium where determined in the Crystal Structure of Rh(Nbd)/Apo-Fr, PDB code: 2zur:
Jump to Rhodium binding site number: 1; 2; 3;

Rhodium binding site 1 out of 3 in 2zur

Go back to Rhodium Binding Sites List in 2zur
Rhodium binding site 1 out of 3 in the Crystal Structure of Rh(Nbd)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 1 of Crystal Structure of Rh(Nbd)/Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Rh48

b:33.2
occ:1.00
RH X:C4R48 0.0 33.2 1.0
O X:HOH358 2.1 31.0 1.0
O X:HOH356 2.1 31.7 1.0
SG X:C4R48 2.2 24.0 1.0
O X:HOH357 2.3 35.3 1.0
OE2 X:GLU45 2.3 20.1 0.7
C12 X:C4R48 2.4 26.0 1.0
C11 X:C4R48 2.7 27.4 1.0
C13 X:C4R48 3.1 27.1 1.0
C15 X:C4R48 3.1 25.9 1.0
CD X:GLU45 3.2 21.3 0.7
CB X:C4R48 3.3 18.1 1.0
OE1 X:GLU45 3.4 25.1 0.7
C10 X:C4R48 3.5 26.5 1.0
OD1 X:ASP38 3.9 20.3 1.0
O2 X:EDO191 4.3 34.2 1.0
C2 X:EDO191 4.3 36.2 1.0
CG X:ASP38 4.4 16.3 1.0
C16 X:C4R48 4.4 26.1 1.0
CB X:ASP38 4.6 12.4 1.0
C17 X:C4R48 4.6 27.6 1.0
CG X:GLU45 4.6 17.6 1.0
CA X:C4R48 4.7 17.2 1.0
O X:GLU45 4.7 12.9 1.0
CA X:GLU45 5.0 12.5 1.0
C X:C4R48 5.0 17.0 1.0

Rhodium binding site 2 out of 3 in 2zur

Go back to Rhodium Binding Sites List in 2zur
Rhodium binding site 2 out of 3 in the Crystal Structure of Rh(Nbd)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 2 of Crystal Structure of Rh(Nbd)/Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Rh182

b:47.7
occ:0.60
NE2 X:HIS49 1.9 28.0 1.0
CE1 X:HIS49 2.9 28.5 1.0
CD2 X:HIS49 3.0 25.5 1.0
ND1 X:HIS49 4.0 28.4 1.0
CG X:HIS49 4.1 20.6 1.0
O X:HOH313 4.9 46.1 1.0

Rhodium binding site 3 out of 3 in 2zur

Go back to Rhodium Binding Sites List in 2zur
Rhodium binding site 3 out of 3 in the Crystal Structure of Rh(Nbd)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 3 of Crystal Structure of Rh(Nbd)/Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Rh183

b:46.1
occ:0.20
NE2 X:HIS114 2.1 33.3 1.0
O X:HOH192 2.6 57.9 1.0
CE1 X:HIS114 2.9 33.6 1.0
CD X:CD179 3.2 59.0 0.1
CD2 X:HIS114 3.3 32.4 1.0
CB X:CYS126 3.5 32.1 1.0
O X:CYS126 3.8 32.6 1.0
C X:CYS126 4.0 32.2 1.0
ND1 X:HIS114 4.1 32.9 1.0
CA X:CYS126 4.2 31.8 1.0
CG X:HIS114 4.3 30.8 1.0
CB X:GLU130 4.7 34.6 1.0
N X:ASP127 4.8 32.6 1.0

Reference:

S.Abe, K.Hirata, T.Ueno, K.Morino, N.Shimizu, M.Yamamoto, M.Takata, E.Yashima, Y.Watanabe. Polymerization of Phenylacetylene By Rhodium Complexes Within A Discrete Space of Apo-Ferritin J.Am.Chem.Soc. V. 131 6958 2009.
ISSN: ISSN 0002-7863
PubMed: 19453195
DOI: 10.1021/JA901234J
Page generated: Wed Dec 16 02:07:33 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy